From Aura to Shadows
by NanookAttica
Summary: A dark organization known only as the League of Shadows has arisen, working on something they call the "Noble Experiment", combated by the Guardians of the Aura, a secret society. Meanwhile a boy with no memory embarks on his Hoenn League Journey.
1. Prologue

**FROM AURA TO SHADOWS**

**DISCLAIMER - DO I OWN POKEMON? Unfortunately, no. **

**Author's note- This is my first fan-fic on ; the story is ranked T for now, just in case. Tell me if I should change the rank. Anyway, I'm just gonna start the Prologue.**

**PROLOGUE**

The city was dark and unnaturally quiet, the silence broken only by the patter of feet on cobblestone. No humans were anywhere in sight.

Yet it was not a human who was creating the sound.

It was a Pokemon, but it was about human size. If Egyptian myths existed in this world, one could relate his looks to that of Anubis, god of death.

The creature running was a lone Lucario, its arms trailing behind it in the tradition position. The Lucario sprung off of its right foot, sailing through the humid air at least ten meters before landing again. The blue humanoid didn't even hesitate as he hit the ground; he simply kept running.

Eventually silhouettes of other Pokemon were visible racing along the flat rooftops overhead. The Lucario glanced up, seeing his pursuers and pressing on all the faster. Soon he saw an alleyway to his left and dove nimbly into the dark passage, rolling with the impact.

He shot through the alleyway faster than he would have thought, emerging in a new section of the city. Instantly he knew he had been tricked.

"Dammit," the Lucario muttered, looking up at the enclosed area around him. The pavement extended in a square around him, and several dumpsters lined the edge of the area. But what made him spit out the profanity was not these facts. Rather, it was the twenty foot tall brick walls that completely enclosed the area.

Heat blossomed along his back and he was flung forward, flinching at the bone jarring impact as he slammed into the pavement. He turned awkwardly to see his pursuers spread out in a loose formation behind him, the Hydreigon who had used the fire blast attack standing a little ways in front of the others.

The Hydreigon floated a little closer, and the two mortal enemies glared daggers at each other. "Do you have anything to say before you die?" he hissed.

Lucario looked from the Hydreigon to the assembled forces behind him, then said, quite mildly, "F_ you."

No sooner were the two words out of his mouth than the Hydriegon struck with a lightning fast Slam attack that, despite the type disadvantage, knocked the already weakened jackal Pokemon out instantly.

The Hydreigon stared down at his fallen foe, then gestured at the nearby Tyranitar to drag away the body. "Bring him," he snapped. "Then we will force him to tell us what he want to know."

Lucario's eyes opened quite slowly, and he found himself in a very empty concrete room. He felt his neck being clasped very tightly by the Tyranitar who had dragged him away, and saw an Umbreon standing close nearby. That wasn't what scared him. Rather, it was the fact that he was suspended three inches over a tank of water that he was sure would be ice cold.

Waterboarding was a method of torture that was near unbearable. If he didn't tell his enemies everything they wanted to know, the Tyranitar would lower him so that his nose and mouth were just under the surface of the water. Lucario knew it would be near unbearable.

The Umberoen sprang forward so that he was eye to eye with Lucario. "What were you doing?" he asked softly.

There was no point in lying. "I was following Mewtwo."

"Why?"

Lucario couldn't resist. "To see where he went!"

The jibe was a mistake. Instantly, the Tyranitar who held him captive shoved his head forward.

It was worse than death.

Lucario tried to scream, and instantly water rushed in to fill his mouth. INstantly all thoughts of taking this calmly were forgotten, replaced by insanity. Lucario kicked and trashed for at least fifteen seconds before his captor yanked his arm back and he was freed from the deathly clutches of the freezing liquid.

"I will ask you again," the Umbreon said in that same uncaring tone. "And you will not answer me like that again."

Lucario nodded. All of his pride was gone, and he shivered miserably. His only wish now was that death came quickly.

Dewford Town was quiet except for the sound of waves lapping gently across the sands of the beach. Yet Brawly did not hear this, as he was facing an extremely dangerous opponent on the beach, his features twisted in an expression of fierce concentration.

"Who are you?" he demanded.

His opponent smirked, though Brawly couldn't see the movement behind the hood and black face coverings.

"I must admit, you are skilled. Defeating Shade was an easy task, as she is new and has much to learn. I am more intrigued with your victory over Cobra. However you are a Gym Leader. I am intrigued...but not impressed." The man's voice was awful to hear, like rock scraping across cold metal.

"Spare me the banter." Brawly's voice didn't quaver. "Leave Dewford Town in peace."

A chuckle came from the darkness, but there was no other response.

"Very well," Brawly said, plucking a PokeBall from where it rested on his belt. "I will have to force you."

"I must warn you, Gym Leader. I am no pushover."

Brawly said nothing as he threw his PokeBall. "Hariyama, let's do this!" The beach was suddenly illuminated by the light that emanated from the opening PokeBall.

The other man said nothing as he tossed out his own Pokemon; a Bisharp. Brawly grinned. The four times type advantage meant this would be an easy match. He was dead wrong.

"Hariyama, arm thrust!" he ordered. His Pokemon surged forward, bellowing a battle cry of his own name. His opponent said nothing, but his Bisharp reacted with uncanny speed. One second it was in the line of fire, the next it was gone, standing by the side of it's master. The Arm Thrust sliced through empty air.

Brawly grimaced, then shouted, "Again!" Hariyama surged forward.

The man said quietly, "Sucker Punch."

Instantly the Bisharp was in front of Hariyama, delivering an unnaturalypowerful move. Hariyama was thrown backwards twenty feet before skidding across the beach, leaving a deep trench in the sand.

The man glanced at the defeated Pokemon, then said in the same tone, "For your own safety, stay out of our way. You have no idea of the power of the League of Shadows."

With that, he turned and walked away.

Hope you all liked it! I will hopefully be writing a lot more soon, please review!


	2. Chapter I: Determined

**FROM AURA TO SHADOWS**

**So yeah, here's the first chapter.**

**Windy Rain, basically bad, but it depends on your perspective.**

**Anyway, to heck with all of that...for now**

**Chapter I**

**...**

It was the sun that woke him.

Beating down fiercely on his face, the sun forced the boy to sit up, which he did not want to do. He was content with what he was doing; sleeping.

Yet the sun was relentless, and he stood slowly. That was when shock struck him. Suddenly, he realized that he didn't know where he was. What had he been doing? And then he realized there was a blankness in his mind, an empty drawer where his memories should have been,

"Oh my God," he whispered, losing his balance. He fell to his knees, struck silent by the shock of what had happened.

Many people believe that you feel normal after you have amnesia, but this is not the case. You feel like your missing something at the very core of your being, and it haunts you. For many it is too much to bear.

"Can I help you?" a gentle voice said. He turned to see a girl smiling at him, possibly two or three years older then him. He stared at her uncertainly, and the girl laughed. "It's all right," she reassured him. "I won't hurt you. My name's May. What's yours?"

She helped him struggle to his feet once more. "Um..." his voice trailed off. "I can't really remember."

May's eyes widened sympathetically. "Amnesia, huh?" When he nodded, she smiled. "Don't worry," she told the dark brown haired boy. "I'll take you to Professor Birch; he'll know what to do."

She led him through a small town, chuckling softly as he gaped at their surroundings. "Where are we?" he asked.

"In a town called Littleroot," May explained. "It's where I live. At least, in between contests."

"Contests?"

"Pokemon Contests," she replied to the confused boy. He frowned; he felt like he knew the term from somewhere. Suddenly, they stood in front of a larger building. "This is it!" May told him.

The Professor greeted them warmly, and May explained the situation. Birch frowned. "I'm sorry..." his voice trailed off. "Excuse me, I don't even know your name. What is it?"

A single word floated in the boy's mind. A name?"

"He doesn't rememb-" May started, but the boy cut her off.

"It's Nanook," he said, now sure of the fact. Birch smiled a little at that.

"Very well," he said. "As I was saying, I'm sorry I can't bring back your memory. Nor do I know anything about you." He saw Nanook sigh a little, and plunged ahead. "However, I think I might know what might help." Muttering to himself, the researcher walked over to a set of drawers and retrieved three PokeBalls. "Going on a journey will strengthen your resolve as a trainer and a friend," he told the boy. "Perhaps that could strengthen your mind and heart so that you would begin to remember."

Nanook seized the opportunity gladly. "Great!" he replied enthusiastically. Birch threw out the PokeBalls, revealing a Treeko, Torchic, and Mudkip, the traditional starters of the Hoenn region. After inspecting each with his new PokeDex, Nanook retrieved Mudkip's PokeBall. The Professor smiled down at him.

"A good choice, if I don't say so myself," he mused.

"Mudkip, return!" Nanook said, and Mudkip dissolved into a hazy cloud of red light, sucked into the PokeBall in the form of a beam.

The Professor handed him a set of five PokeBalls. May stepped forward. "Nanook, I'll come with you as far as Oldale Town," she told the brown eyed boy. Nanook nodded, and rushed out of the lab, eager to start on his journey. May turned to Birch.

"You know who he reminds me of?" she asked him.

Birch smiled and nodded. "Ash."

**...**

The short route that led to Oldale town was uneventful, and the companions found themselves sitting bored in Oldale's Pokemon Center. Rain poured down outside, causing a deafening patter to drum on the building's roof.

Suddenly, the door flew open and a boy that seemed around Nanook's age burst in. He began walking up the stairs, presumably to his room, when Nurse Joy called to him, noticing the PokeBalls on his belt.

"Don't you want me to heal your Pokemon?" she asked, puzzled.

The boy had deep brown hair that was almost black, contrary to his ice blue eyes. "I'll take care of them myself, thanks."

Nanook was instantly on his feet. "Who do you think you are?" he demanded. "Don't you care about your Pokemon? Nurse Joy is an expert."

The boy looked calmly at Nanook. "Someone has a lot of guts," he remarked, causing Nanook to smolder angrily. He turned to him. "Very well," he said. "If you know so much about Pokemon, then let's have you prove it."

Nanook frowned. "What do you mean?"

"A battle, of course," the boy scoffed. "We can use the indoor stadium."

WIth that, he strode off down the hallway that lead to the stadium, shooting back over his shoulder, "I'm Attica, by the way."

"Nanook," the brown eyed boy spat.

_In the stadium..._

Nanook was pretty confident; May had helped him to learn to battle, even though her own Pokemon were far superior to his Mudkip. He had no doubt that Attica would leave this room defeated.

"The battle will be one-on-one and will end when either sides Pokemon are unable to battle!" May announced from the referee's platform. Nanook grinned.

"Mudkip, it's up to you!" he shouted, throwing his only Pokemon. Mudkip landed neatly on the dirt floor.

"Mudkip!" he announced, excited to be in a battle.

"A starter," Attica noted. "Very well," he said calmly. "I will battle with my first Pokemon as well!" He punctuated the last word by sending a PokeBall flying. It burst open in a flash of white light and a Pokemon Nanook had never seen before stepped onto the field.

"Glaceon, let's do this!" Attica said, obviously confident in his and his Pokemon's ability.

"Mudkip, finish them quickly. Tackle, let's go!" Nanook ordered.

"Kipkipkipkipkip!" Mudkip grunted, running full speed at the unmoving Glaceon.

At the last moment, Attica barked, "Protect!"

Mudkip collided headlong with the green energy shield and fell back dazed.

"Time to wrap this up!" Attica said. "Icy Wind!" Glaceon opened her mouth and hail flew out, propelled by a fierce gust of wind. The attack smashed into Mudkip, leaving the water-type knocked out.

Attica glanced from the Pokemon to its trainer before finally saying in that same, infuriatingly calm tone, "It wasn't the Pokemon that was the reason you lost." With that, he turned and walked away, leaving Nanook staring numbly at his hurt friend.

**...**

**Hopefully it was pretty good. Yeah I know the names are kind of weird, but it'll be explained later.**

**Please review, and there's more to come!**


	3. Chapter II: Veni, Vidi, Vici

**FROM AUARA TO SHADOWS**

**Yeah, so this is Chapter 2. People please review because this...IS...**_**SPARTA! **_**I'm weird, I know...but hey...whatever. **

**Chapter II**

**Attica: Veni, Vidi, Vici**

**(That's "I came, I saw, I conquered, for all you non-Latin speaking folk)**

**...**

May approached Nanook nervously, wondering about what his reaction would be to his crushing defeat. "Nanook..." she began. "I'm really sorry that-"

Nanook turned to face her and she was relieved to see that he was grinning. "Don't be," he told the older girl. "I've learned a lot, and next time I battle Attica, he is so freaking going down!" Snatching up his PokeBall, Nanook charged out of the room, presumably to Nurse Joy for her to heal Mudkip.

May smiled. _It looks like someone has a rival, _she thought to herself.

**...**

Nanook lay in a field in Oldale town, just reflecting. Mudkip lay curled up at his feet, and the two friends watched the clouds meander across the striking blue sky. Nanook thought back to his defeat, reliving every moment of the battle, seeing what he did wrong. He would like to blame his failure on the fact that Attica's Glaceon was obviously powerful, and had battled many times before. But he also knew it was mostly his fault.

_Be at one with your Pokemon, _a voice whispered in his head. _Trust your instincts, do not over predict. _

Nanook sat straight up. "Who said that?" There was no reply.

"Excuse me," a feminine voice said from behind him. Nanook whirled to see a girl that looked about his age. "Nobody said anything; who were you talking to?"

"Um..." Nanook's voice trailed off. The girl was strikingly beautiful; ayt least, in his opinion. "I forget," he finished lamely.

The girl laughed softly, a soothing sound. "My name's Dawn," she announced.

"Nanook," he replied.

Dawn tilted her head questioningly. "That's an odd name."

Nanook shrugged. Suddenly, he saw movement behind Dawn and looked past her, his heart plummeting to the pit of his stomach.

Attica was striding towards them, eating up the distance between himself and the two people engaged in conversation. "Dawn," he said, not even acknowledging Nanook's presence. "We need to go."

"You two are traveling together?" Nanook asked, hoping against hope he was wrong.

"Yeah," Dawn said, confirming his fears. Nanook tasted bile rising in his throat, and fought to keep it back.

"Well, nice to have met you," he said, forcing out the words. They tasted sour in his mouth. He turned to his new rival, now in more ways than one. "And Attica..."

The other boy glanced at Nanook.

"I'm calling for a rematch sometime," Nanook finished. Attica scoffed at him.

"Don't waste your time."

"I plan on winning."

Attica flashed him an exasperated glance. "Fine. Meet me at the Petalburg City Pokemon Center. We'll battle there."

Nanook nodded.

"Come on Dawn," Attica said, leading the girl away. Nanook watched after her until she was out of sight.

**...**

"Dawn," Attica hissed.

"What is it?" she mumbled.

"Get up!" His voice was urgent. Dawn rolled out of bed, glancing at the clock. Half past two in the morning. She repeated her question.

"I have to show you something," Attica replied. "It's important," he added.

She followed him downstairs in the quiet Pokemon Center. He lead her outside into the cold night air. Dawn wished she could have changed out of her pajamas into something warmer.

Attica lead her away from the main part of the town into a less hospitable area.

"What?" She was exasperated, and the word came out more forceful than she would have liked. She turned and gasped in shock. Attica was changing into the form of a Pokemon she recognized from her Sinnoh journeys.

"A Zoroark!" she exclaimed. The dark type grinned and extended its claws. Suddenly Dawn realized she was in danger. She turned to run but felt strong arms throw her down. SHe had no chance of escaping.

A figure emerged from the gloom, a man dressed in a material that was patterned after something that reminded her of snakeskin. "I am Cobra," he announced in a silky voice.

"Good for you," Dawn said. The Zoroark punched her and she gasped for breath, winded.

"There is no need for that," Cobra cooed, shooing away the Pokemon. He ran one soft hand across Dawn's cheek. "All I need is what you know about the Orb."

Dawn frowned. "I don't know what you're talking about," she answered truthfully. Cobra scowled.

"I think you do," he persisted, dragging her to her feet.

"I really don't," she replied, hand slinking towards her PokeBalls. Then she mentally kicked herself; her PokeBalls were in her room!

Cobra cursed. "If you cannot give me what I want to know, you don't think I'm just going to let you go." As an afterthought, he added, "You really are quite pretty." Dawn stared at him, disgusted. The man was probably in his twenties, probably ten years older than her!

"Let me go," she insisted.

"Only if you give me what I want," Cobra shot back.

Her heart sank as she realized what Cobra wanted. She tried to turn and run but his hand closed around her collar.

"Stay here," he cooed. Dawn struggled fiercely but to no avail.

"Let me go, you son of a-"

"DRAGONITE!"

The raucous call exploded through the alleyway as that same Pokemon erupted from the end of the alleyway, slamming into Cobra and yelling that same battle cry again. Dawn stared in shock. Cobra, struggling under the weight of the large Pokemon, cursed.

"You Aura-loving idiots!" he snapped. Then he whistled high and shrill, and more Pokemon emerged; a Hydreigon, Tyranitar, Umbreon, and a Gengar. Cobra threw a PokeBall and a Seperior emerged, yelling in anger and fury.

Yet the Dragonite was not alone either. A few more Pokemon charged down the alleyway and engaged Cobra's forces. Utter chaos engulfed the alley and elemental attacks flew wildly.

Dawn turned to run, shocked and confused by what was hapening. However, once she reached the end of the long alleyway, a Pokemon leapt in front of her. It was an Umbreon. The Umbreon's eyes flashed blue; Dawn recognized the attack! It was Amnesia.

And then darkness engulfed her.

**...**

"Dawn," Attica said. "Wake up."

Dawn, rested from an uneventful night, got out of bed and looked out the window. The sun had already risen, and a golden glow covered the fields of Oldale town. Suddenly, Dawn got a strange feeling, as if she had forgotten something important. Then she shrugged and pushed the feeling away; it was probably nothing.

She went into the bathroom and got dressed in her usual outfit. Attica was already ready to go, so she retrieved her PokeBalls from beside her bed and proceeded downstairs with her traveling companion. Waving good-bye to Nurse Joy, they left the Pokemon Center.

"Where to next?" Dawn asked.

"Petalburg City," Attica answered. "There's a Gym there, as well as my second victory over Nanook."

Dawn frowned. "Isn't the Gym there really hard?"

"Not to me and Glaceon," Attica scoffed. "It'll be a breeze."

As they left Oldale town, neither noticed a trainer standing on a rooftop far above, the wind blowing his blue traditional clothes behind him. Next to him stood a Pokemon; a jackal like fighting and steel type.

"Things are getting interesting, aren't they, Lucario?" Riley asked his partner.

"Lucar," the Pokemon agreed.

Suddenly Riley noticed the two trainers walking out of the town far below. "Those are the two we're supposed to follow, right?" Lucario confirmed the answer with a nod. The two silently began to follow a ways behind Attica and Dawn. Riley had a strange feeling that they weren't the only ones doing just that.

**...**

May had told Nanook that she was just going to bring him to Oldale town, but she had changed her mind once he had told her that his next destination was Petalburg city. That was, after all, where her parents and brother lived. She decided to continue with Nanook until they reached Petalburg. She had told the younger boy that she was doing this so she could visit her family. What she hadn't told him was that she also wanted to travel with him to make sure his crushing defeat didn't keep him down. So far, May as happily surprised that this seemed to not be the case.

Now they were traveling along an area surrounded by trees on either side, with a large pond to their right. May had informed Nanook that this was route 102.

Nanook had just won his first victory against a kid named Calvin who had used a Zigzagoon, and he was still psyched. All he wanted now was to catch his first Pokemon. It seemed that was to be the case, as a Pokemon the trainer had never seen before waddled across their path. Nanook scanned it with his PokeDex.

"Seedot," the PokeDex beeped in a monotone voice. "It hangs off branches and absorbs nutrients. When it finished eating, its body becomes so heavy that it drops to the ground with a thump."

Nanook grinned and put away the machine. "Mudkip, come on out!" he yelled, throwing the red and white ball into the air. It split open with the familiar wooshing sound and, in a beam of light, Mudkip materialized.

"Kip!" Mudkip announced.

"Tackle attack!" Nanook commanded. Mudkip took off running, but just before he made contact, the Seedot glowed silver and Mudkip bounced off.

"That's harden," May advised. "It raises the Pokemon's defense. Stick to special attacks, even if they aren't very effective."

"Water gun!" Nanook shouted. A steam of water erupted from Mudkip's mouth, blasting the Seedot backwards. "Great!" Nanook praised his Pokemon. "Now Mud-Slap, let's go!"

A barrage of mud shot, once again, from Mudkip's mouth, damaging the weakened Seedot even more.

"Now!" May instructed.

Nanook threw a PokeBall and Seedot was swept inside. The PokeBall began to roll. Once...twice...three...

In a ding and a sparkle, Seedot was caught. Nanook bent over and retrieved the PokeBall.

**...**

Hidden in the trees, two figures observed Nanook's celebration.

"An interesting character," the taller of the two admitted in a soft voice. He was dressed like a ninja, in all black. He even had a sword slung across his back.

"Kind of cute, isn't he?" the other, a young girl of Nanook's age, murmured to herself.

"Focus, Shade," the man reprimanded. "We're supposed to be gathering information."

Shade rolled her eyes. "I know that."

"Listen," the man said. "The League of Shadows thinks that that is the one."

Shade drew in a breath. "Really? Him?"

The man nodded. "That is why we are following him, and, if the need arises..." He looked out to where May and Nanook were continuing down the route, still chattering about the Seedot. "...we will kill him," he finished.


End file.
